Strike Witches doujin parody on Senko no Ronde. It'd be so delicious and godlike.
Negima would be a legit jRPG (they already use mad RPG references as it is) if they worked off of the manga rather than the anime (due to more content). They have a story laid out already that starts out as small time kid following in his heroic dad's footsteps and eventually leading up to epic saving the world type shit. They have a huge and diverse cast of characters from multiple classes. It's already perfect.
Deadman Wonderland (didn't they make that an anime yet?) would be an easy candidate for 2d fighter. I mean, it practically is one already, the way they're forced to do arena style 1v1 battles and how they each have unique special blood techniques (shots/blades/bombs/whips/armor/etc).
Also, show me a fucking Elfen Lied brawler. Shit would be so badass to just tear up bitches as Lucy. Taking from the entire story (aka: the manga) would be a must though, or else you'd lose out on awesome shit like that dude who shoots morning stars, the diclonius factory, or the giant head thing.
Also also, it came from VN (and I've probably mentioned it before), but I think Fate/Stay Night's concept (grail wars, summon legendary heroes to win, etc) would be good as a DotA or Bloodline Champions type game, but 7p free for all rather than team based.